Located on the eastern bank of the Jordan River, 9 kilometres (5.6 mi) north of the Dead Sea and 10 km (6.2 mi) southeast of Jericho. The entire site, which is spread over an area of 533.7 hectares (5.337 km2; 1,319 acres), has two distinct zones – Tell al-Kharrar, also called Jabal Mar Elias (Elijah's Hill), and the area close to the river (2 km (1.2 mi) to the west), the Zor area, where the ancient Church of Saint John the Baptist is situated.

The site is close to the ancient road between Jerusalem and Transjordan, via Jericho, across a Jordan River ford and connecting to other biblical sites such as Madaba, Mount Nebo and the King's Highway.

While the initial site of veneration was on the eastern side of the River Jordan, the focus had shifted to the western side by the 6th century. The term Al-Maghtas has been used historically for the area stretching over both banks of the river. The western part, also known under the name Qasr el-Yahud, has been mentioned in the UNESCO proposal, but so far has not been declared as a World Heritage Site.